Hello Christopher,
I see that this was also posted at SeqAnswers yesterday. I searched and
didn't see anything specifically in the manual or at seqanswers that
addresses this (but if someone else can find it, please add to this thread):
http://seqanswers.com/forums/showthread.php?t=20084
Do you think this is a problem with the Cuffmerge program itself? If so,
going to the authors is the next step by emailing [email protected]
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results
(See: /Example/: *unexpected results with* /*RNA-seq analysis*/ *tools.)*
*
*If you think this is a problem may be with the Galaxy wrapper around
CuffMerge, we can take a closer look. Please share a link to your
history containing this data. Use "Options (top 'gear' icon in history
panel) -> Share or publish", generate a share link, copy link, and email
link back directly to me. Note the dataset #'s involved and leave all
datasets unhidden/undeleted.
Thanks!
Jen
Galaxy team
On 5/15/12 1:38 PM, Christopher M. Weber wrote:
Hello,
Problem: Cuffmerge loses p_id from reference genome in merged gtf file
on Galaxy online server resulting in blank cds cuffdiff files.
DATA Input to Cuffmerge or Cuffcompare:
Two fly cufflinks transcript assemblies created from bam files in
Galaxy server using reference annotation and bias correction.
Options:
Use Reference Annotation: YES
UCSC DM3 genes gtf (D. melanogaster) or ENSMBL 5.25 genes gtf
Use Sequence Data: YES
Result: tss_id found in cuffmerge but no p_id with either reference
annotation file. Examples included below.
Reference:
2L protein_coding stop_codon 8608 8610 . + 0 exon_number "2";
gene_id "FBgn0031208"; gene_name "CG11023"; p_id "P13746";
transcript_id "FBtr0300689"; transcript_name "CG11023-RB"; tss_id
"TSS8369";
Cuffmerge:
Cufflinks exon 8193 9484 . + . gene_id "XLOC_000001";
transcript_id "TCONS_00000001"; exon_number "2"; gene_name "CG11023";
oId "FBtr0300689"; nearest_ref "FBtr0300689"; class_code "="; tss_id
"TSS1";
2L Cufflinks exon 66721 67003 . + . gene_id "XLOC_000002";
transcript_id "TCONS_00000003"; exon_number "1"; gene_name "dbr"; oId
"CUFF.1.1"; nearest_ref "FBtr0078100"; class_code "j"; tss_id "TSS2";
Help is much appreciated,
Thanks!
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Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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